Visualizing 3D Structures

To view your predicted structure generated by AlphaFold in 3D, you can use Visual Molecular Dynamics (VMD).

Steps:

  • Log onto Open On Demand ( https://rivanna-portal.hpc.virginia.edu/)
  • Choose the ‘Desktop’ interactive app and fill out the webform with your required resources.
  • Click launch.
  • Load VMD in the terminal:
module load vmd
vmd

The VMD windows will launch. From there, you can open your .pdb file from the AlphaFold output directory to view the 3D model (colored by pLDDT).

Loading your .pdb file (a).
Loading your .pdb file (b).
Loading your .pdb file (c).
Loading your .pdb file (d).

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